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Agriculture
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Recent Advances in Breeding, Genetics and Omics of Citrus
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Recent Advances in Breeding, Genetics and Omics of Citrus

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: closed (10 November 2021) | Viewed by 20647

Special Issue Editor

Prof. Dr. Patrick Ollitrault

E-Mail Website
Guest Editor
Unité Mixte de Recherche Amélioration Génétique et et Adaptation des Plantes (UMR AGAP) Corse, Centre de coopération Internationale en Recherche Agronomique pour le développement (CIRAD), 20230 San Giuliano, France
Interests: genetics; genomics; evolution; polyploidy; reproductive biology; QTL analysis; breeding

Special Issue Information

Dear Colleagues,

As a result of climate change, the global citrus industry faces increasing biotic and abiotic constraints, while consumers expect higher quality products and public policies in many countries call for more environmentally friendly farming practices. In this context, rootstock and scion breeding is an essential component in building the citrus industry of the 21st century. For a long time, citrus breeding was hampered by biological constraints, such as partial apomixis, self-incompatibility, the complex or unknown interspecific origins of most horticultural groups, as well as a lack of knowledge on the genetic determinants of useful traits. Today, new biological knowledge and recent developments in the fields of biotechnology and genomics have helped overcome many of these issues.

The aim of this Special Issue is to highlight recent advances in fundamental and applied research in the fields of citrus breeding, reproductive biology, genetics, genomics, and physiology, which contribute to tackling the challenges faced by the citrus industry. We welcome novel research articles and reviews on: (1) the phenotypic and molecular characterization of citrus germplasm and the phylogeny of citrus; (2) reproductive biology; (3) ecophysiology, physiology, and the molecular mechanisms of adaptation to biotic and abiotic stresses and fruit quality; (4) QTLs and association genetics; (5) the role of transposable elements in phenotypic diversity; (6) new methodologies for citrus breeding, such as ploïdy manipulation, marker-assisted selection, genomic selection, biotechnologies, and innovative phenotyping methods; and (7) detailed evaluations of agronomical performances and qualities of new cultivars and rootstock.

Prof. Dr. Patrick Ollitrault
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Citrus
  • Disease resistances
  • Abiotic stress adaptation
  • Fruit quality
  • Rootstock breeding
  • Cultivar breeding
  • Reproductive biology
  • Physiology
  • Phenotyping
  • Genomics
  • Biotechnology
  • Association genetics
  • Polyploidy
  • QTL analysis
  • Marker assisted selection
  • Genomic selection

Published Papers (6 papers)

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Research

25 pages, 2479 KiB  
Article
Comparative Transcriptome Profiling of Salinity-Induced Genes in Citrus Rootstocks with Contrasted Salt Tolerance
by Hager Snoussi, Hend Askri, Diana Nacouzi, Imen Ouerghui, Anthony Ananga, Asma Najar and Walid El Kayal
Agriculture 2022, 12(3), 350; https://doi.org/10.3390/agriculture12030350 - 28 Feb 2022
Cited by 4 | Viewed by 3074
Abstract
Salinity is one of the most destructive environmental challenges for citriculture worldwide, and all climate change scenarios are predicting an increased impact of salinity on citrus orchards. Citrus cultivars are grown as grafts on various rootstocks to provide specific adaptation to abiotic stress [...] Read more.
Salinity is one of the most destructive environmental challenges for citriculture worldwide, and all climate change scenarios are predicting an increased impact of salinity on citrus orchards. Citrus cultivars are grown as grafts on various rootstocks to provide specific adaptation to abiotic stress and tolerance to major diseases such as citrus tristeza virus. To understand rootstock–scion interactions with regard to salinity, transcriptome profiling of mRNA expression was analyzed for 12 candidate genes in leaves, shoots, and roots of five Hernandina clementine scions grafted on Rangpur lime (LR), Volkamer lemon (CV), Carrizo citrange (CC), sour orange (Big), and Cleopatra mandarin (MC) rootstocks in response to moderate and severe salinity. qRT-PCR analysis revealed differential gene expression that varied by rootstock, salinity level, and tissue. The majority of induced genes were those involved in ion transporter proteins (mainly NHX1 and HKT1 genes), Cl− homeostasis (CCC1 gene), biosynthesis and accumulation of compatible osmolytes, proline (P5CS gene) and glycine betaine (CMO gene), accumulation of proteins (LEA2 gene), and ROS scavenging antioxidant activity (mainly APX). We show that these expression patterns could explain the relative tolerance of the used rootstocks and report new insights on the main salt tolerance mechanisms activated by these rootstocks. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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19 pages, 3547 KiB  
Article
Breakdown of Self-Incompatibility in Citrus by Temperature Stress, Bud Pollination and Polyploidization
by Rafael Montalt, Laura Prósper, María Carmen Vives, Luis Navarro, Patrick Ollitrault and Pablo Aleza
Agriculture 2022, 12(2), 273; https://doi.org/10.3390/agriculture12020273 - 15 Feb 2022
Cited by 6 | Viewed by 4222
Abstract
Self-incompatibility (SI) is present in around half of all species of flowering plants. SI limits endogamy and contributes to increased genetic diversity. SI is a very important trait in citrus because, when coupled with parthenocarpy, it allows seedless fruit production. Otherwise, SI is [...] Read more.
Self-incompatibility (SI) is present in around half of all species of flowering plants. SI limits endogamy and contributes to increased genetic diversity. SI is a very important trait in citrus because, when coupled with parthenocarpy, it allows seedless fruit production. Otherwise, SI is an impediment to genetic studies and breeding programs. Temperature stress, bud pollination and polyploidization can induce the breakdown of the SI mechanism in several species. In this work, we investigated how the SI mechanism can be broken down in two self-incompatible diploid citrus genotypes: ‘Fortune’ mandarin and ‘Clemenules’ clementine. The influence of temperature stress on the SI mechanism was assessed in self-pollinated flowers of ‘Fortune’ mandarins subjected to 2 temperature regimes (10 °C and 30 °C), whereas the bud pollination effect was investigated in the same genotype and in ‘Clemenules’ clementines cultivated under field conditions. The tetraploid ‘Clemenules’ clementine cultivated under field conditions was used to study if tetraploidization can bypass the SI reaction. Histological observations of pollen tube growth and seed production in self-pollinated flowers were used to evaluate the breakdown of SI, while the genetic analysis with SSR and SNP markers confirmed that all recovered plants were zygotic and had been originated by selfing. Our results confirm that the SI reaction can be surpassed by temperature stress, bud pollination and tetraploidy. To our knowledge, this is the first report in citrus in which the SI reaction breakdown by these three different strategies is demonstrated by molecular markers. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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13 pages, 1537 KiB  
Article
Influence of the Rootstock and the Ploidy Level of the Scion and the Rootstock on Sweet Orange (Citrus sinensis) Peel Essential Oil Yield, Composition and Aromatic Properties
by Vincent Ferrer, Noémie Paymal, Carole Quinton, Gilles Costantino, Mathieu Paoli, Yann Froelicher, Patrick Ollitrault, Félix Tomi and François Luro
Agriculture 2022, 12(2), 214; https://doi.org/10.3390/agriculture12020214 - 1 Feb 2022
Cited by 8 | Viewed by 2380
Abstract
Rootstock is widely used for the cultivation of citrus fruits because it brings resistance or tolerance to diseases or environmental constrains and modulates the fruit quality. Polyploidization is a widespread improvement strategy in citrus. The objective was to evaluate the effect of rootstock [...] Read more.
Rootstock is widely used for the cultivation of citrus fruits because it brings resistance or tolerance to diseases or environmental constrains and modulates the fruit quality. Polyploidization is a widespread improvement strategy in citrus. The objective was to evaluate the effect of rootstock and ploidy level on the composition of essential oils. Two trials were conducted, one displaying a ‘Navelina’ orange grafted on three rootstocks and a second combining two ploidy levels (di and tetraploid) of scion (‘Pineapple’ orange) and rootstock (‘Carrizo’ citrange). The composition of peel essential oil (PEO) was analyzed by gas chromatography coupled with mass spectrometry, and a panel of experts analyzed its flavor variation with a triangle test approach. The rootstock influenced the yield and composition of the orange PEO, with a low impact on flavor. Neither the rootstock nor the scion ploidy level affected the PEO yield. Only the tetraploid level of the scion significantly modified the PEO composition, reducing the oxygenated compound fraction. Sensitive significant differences were detected between the reference sample (diploid scion–diploid rootstock) and the three other combinations. These results suggest that for the profiling of an aromatic flavor, the rootstock is a key element as is the ploidy level of the scion. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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26 pages, 4012 KiB  
Article
Genomic Instability in Somatic Hybridization between Poncirus and Citrus Species Aiming to Create New Rootstocks
by Dominique Dambier, Pascal Barantin, Gabriel Boulard, Gilles Costantino, Pierre Mournet, Aude Perdereau, Raphaël Morillon and Patrick Ollitrault
Agriculture 2022, 12(2), 134; https://doi.org/10.3390/agriculture12020134 - 19 Jan 2022
Cited by 5 | Viewed by 3556
Abstract
Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or [...] Read more.
Rootstocks are an important component for citrus adaptation to increasing biotic and abiotic stresses resulting from global climate change. There is a strong complementarity between Citrus species, which adapt to abiotic stresses, and Poncirus trifoliata and its intergeneric hybrids, which exhibit resistances or tolerances to major diseases and pests. Thus, symmetrical somatic hybridization between complementary diploid rootstocks of these two genera appears to be an efficient way to develop new tetraploid rootstocks in order to address the new challenges of the citrus industry. New intergeneric somatic hybrids were obtained by electrofusion between protoplasts of Citrus and P. trifoliata hybrids. Extensive characterization of the nuclear and cytoplasmic genomes was performed by genotyping-by-sequencing (GBS) analysis. This revealed diploid cybrids and nuclear somatic hybrids. Mitochondrial genomes were mostly inherited from the callus parent, but homologous recombination events were observed for one parental combination. Chloroplasts exhibited random uniparental inheritance. GBS revealed local chromosomal instabilities for all nuclear somatic hybrids and whole chromosome eliminations for two hybrids. However, at the whole genome level, symmetrical addition of the nuclear genomes of both parents was predominant and all somatic hybrids displayed at least one trifoliate orange haplotype throughout the genome. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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21 pages, 20300 KiB  
Article
Graft Compatibility Classification within Aurantioideae Based on Biometric Traits and the Anatomy of Graft Union
by Laudecir Lemos Raiol-Junior, Everton Vieira de Carvalho, Alécio Souza Moreira, João Paulo Rodrigues Marques, Eduardo Sanches Stuchi, Leandro Peña and Eduardo Augusto Girardi
Agriculture 2022, 12(1), 76; https://doi.org/10.3390/agriculture12010076 - 6 Jan 2022
Cited by 5 | Viewed by 3418
Abstract
Citrus relatives are a relevant source of valuable traits for use in citrus breeding, including resistance to diseases such as Huanglongbing (HLB). Resistant rootstocks may impact tree responses to HLB. This requires graft compatibility, which has been poorly investigated within the Aurantioideae. In [...] Read more.
Citrus relatives are a relevant source of valuable traits for use in citrus breeding, including resistance to diseases such as Huanglongbing (HLB). Resistant rootstocks may impact tree responses to HLB. This requires graft compatibility, which has been poorly investigated within the Aurantioideae. In this study, the biometric characteristics and the anatomy of the graft union of 86 scion/rootstock combinations were assessed. This comprised 18 genotypes/species and 8 genera from Citrinae, Balsamocitrinae, and Clauseninae subtribes sensu Swingle and Reece. Most graft combinations were found to be noncompatible. Phylogenetic proximity did not ensure successful grafting as, for example, Orange jasmine autografts failed, whereas some intergeneric grafts were successful (>60% of graft-take). Plant scion height was directly related to graft-take, but the correlation between the scion and rootstock stem diameters was not a reliable indicator of graft compatibility. Rangpur/Tabog, Tabog/Rangpur, Wampee/Rangpur, Wampee/Pomeroy, Wampee/Swingle, Pomeroy/Wampee, and Swingle/Wampee were the most compatible intergeneric graft combinations. Graft-take success for this was at similar levels to those of sweet orange grafted on common citrus rootstocks. The position as a scion or rootstock in the combination affected the performance and was specific to the genotypes tested. The lack of differentiation between xylem-derived calli and the accumulation of phenolic compounds at the graft union were clear anatomical and biochemical markers, respectively, of incompatibility for most Aurantioideae combinations. In the field, within a set of the ten most promising combinations, Hamlin/Rangpur (control) was the only one that became infected by ‘Candidatus Liberibacter asiaticus’. This was first observed 12 months after planting. Overall, the assessment of biometric traits and anatomy of the graft union allowed Aurantioideae genotypes to be divided into four clusters, with respect to their graft compatibility, as follows: fully compatible with high graft-take and plant growth; potentially compatible with high graft-take but lower plant growth; partially incompatible with lower graft-take and poor plant growth; and fully incompatible with a complete absence of graft-take. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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21 pages, 2264 KiB  
Article
Less Is More: A Hard Way to Get Potential Dwarfing Hybrid Rootstocks for Valencia Sweet Orange
by Danilo Pereira Costa, Eduardo Sanches Stuchi, Eduardo Augusto Girardi, Alécio Souza Moreira, Abelmon da Silva Gesteira, Mauricio Antonio Coelho Filho, Carlos Alberto da Silva Ledo, André Luiz Vanucci da Silva, Helton Carlos de Leão, Orlando Sampaio Passos and Walter dos Santos Soares Filho
Agriculture 2021, 11(4), 354; https://doi.org/10.3390/agriculture11040354 - 15 Apr 2021
Cited by 14 | Viewed by 3088
Abstract
As in several fruit crops, citrus trees with decreased size allow for a higher planting density, which may lead to higher productivity and facilitate operations such as harvesting and spraying. The use of dwarfing rootstocks is one of the most feasible methods for [...] Read more.
As in several fruit crops, citrus trees with decreased size allow for a higher planting density, which may lead to higher productivity and facilitate operations such as harvesting and spraying. The use of dwarfing rootstocks is one of the most feasible methods for tree size control, but few commercial varieties are available to date. In this work, the long-term performance of Valencia sweet orange grafted onto 51 hybrid citrus rootstocks was evaluated in rainfed cultivation at 6.0 m × 2.5 m tree spacing in Northern São Paulo State, Brazil. About a third of the evaluated hybrids were classified as dwarfing and semi-dwarfing rootstocks, that is, respectively inducing a relative canopy volume of <40% and 40–60% compared with the standard rootstock, the Rangpur lime Santa Cruz selection. The production efficiency and soluble solids concentration were conversely related to the canopy volume. Three citrandarins of Sunki mandarin (TSKC) × Flying Dragon trifoliate orange (TRFD) were grouped within the most productive dwarfing rootstocks. Other hybrids that expressively decreased tree size were mainly sensitive to drought; therefore, the mean fruit yield was low, indicating the need for irrigation, albeit fruit quality was high. Estimated productivity on the selected TSKC × TRFD rootstocks would double to an average of 40 t·ha−1·year−1 if tree spacing was adjusted to the smaller tree size. Although the HTR-208 citrandarin and the LCR × CTSW-009 citrumelimonia were as vigorous as the Santa Cruz Rangpur lime, they induced an outstanding fruit yield due to their highest tolerance to drought and, hence, can be considered for rainfed cultivation at wider tree spacing. Full article
(This article belongs to the Special Issue Recent Advances in Breeding, Genetics and Omics of Citrus)
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